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microbial-dynamics

Microbial population dynamics modeling and analysis. Bacterial growth curve fitting (logistic, Gompertz, Baranyi), Lotka-Volterra community dynamics, Gillespie stochastic simulation, biofilm quantification, CFU enumeration, and genome annotation. For metabolic modeling use cobrapy; for sequence analysis use biopython.

backend/cli/skills/biology/microbial-dynamics/SKILL.md

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# Microbial Dynamics: Population Dynamics & Modeling

## Overview

Microbial Dynamics provides computational tools for modeling and analyzing microbial populations. This skill covers bacterial growth curve fitting using standard models (logistic, Gompertz, Baranyi), multi-species community dynamics via Lotka-Volterra equations, stochastic population simulation using the Gillespie algorithm, biofilm quantification from crystal violet assays, colony-forming unit enumeration with statistical analysis, bacterial genome annotation via Prokka, and simplified anaerobic digestion modeling.

## When to Use This Skill

- Fitting bacterial growth curves from OD600 time-series data
- Extracting growth parameters: lag phase duration, maximum growth rate (mu_max), carrying capacity (K)
- Modeling multi-species microbial community interactions
- Running stochastic simulations of gene expression or population dynamics
- Processing crystal violet biofilm assay data
- Calculating CFU/mL from serial dilution plating